Investigation of the Genetic Structure of Some Common Bean (Phaseolus vulgaris L.) Commercial Varieties and Genotypes Used as a Genitor with SSR and SNP markers

Common bean is a species belonging to the Phaseolus genus of the Leguminosae family. It has economic importance due to being rich in protein, vitamin A and C, and minerals. Being one of the most cultivated species of legumes, the determination of genetic diversity in bean genotypes or populations has an important role in terms of our genetic resources. The objective of this study was to evaluate the genetic structure of 94 genotypes which were cultivated in different parts of the world and our country with SSR and SNP markers. 10 SSR loci and 73 SNP primers were used for the determination of genetic structure in commercial cultivars and breeding lines. All of the SSR and SNP loci used in the study were found to be polymorphic. A total of 89 alleles were identified for 10 SSR loci. Mean number of alleles per locus (Na=8.9), effective allele number (Ne=3.731), Shannon information index (I=1.468), observed heterozygosity (Ho=0.023), and expected heterozygosity (He=0.654) were calculated based on SSR analysis. According to the results of Bayesian-based STRUCTURE analysis using SSR and SNP data, 94 bean genotypes were genetically divided into three main clusters. According to genetic similarity based UPGMA dendrogram obtained from SSR and SNP analysis, 94 bean genotypes were divided into 2 main clusters. The obtained results provide important information about the genetic structures of the studied bean cultivars and breeding lines. With the obtained results, it will be possible to develop breeding programs to develop new cultivars by using our gene resources.

Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map

Roses are highly valuable within the flower industry. The metabolites of anthocyanins, flavonols, and carotenoids in rose petals are not only responsible for the various visible petal colors but also important bioactive compounds that are important for human health. In this study, we performed a QTL analysis on pigment contents to locate major loci that determine the flower color traits. An F1 population of tetraploid roses segregating for flower color was used to construct an ultra-high-density genetic linkage map using whole-genome resequencing technology to detect genome-wide SNPs. Previously developed SSR and SNP markers were also utilized to increase the marker density. Thus, a total of 9,259 markers were mapped onto seven linkage groups (LGs). The final length of the integrated map was 1285.11 cM, with an average distance of 0.14 cM between adjacent markers. The contents of anthocyanins, flavonols and carotenoids of the population were assayed to enable QTL analysis. Across the 33 components, 46 QTLs were detected, explaining 11.85–47.72% of the phenotypic variation. The mapped QTLs were physically clustered and primarily distributed on four linkage groups, namely LG2, LG4, LG6, and LG7. These results improve the basis for flower color marker-assisted breeding of tetraploid roses and guide the development of rose products.

Identification of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) that are associated with the nectariless trait of Gossypium hirsutum L

Cotton (Gossypium hirsutum L.) has nectar containing modified stomates called nectaries that can be located on leaves, bracts or calyces. The nectar attracts some beneficial insects such as bees, but also predatory damaging insects such as heliothines and Lygus species. There is a naturally occurring mutation that eliminates the nectar containing nectaries and makes the cotton plants less attractive to insects. The nectariless (ne) trait is associated with a double recessive mutation of two genes (ne1 and ne2) on homeologous chromosomes 12 and 26. Expression of the trait can be variable and is also affected by environmental conditions. This makes accurately selecting for the trait based on phenotype difficult. This study identified SSR and SNP markers that can be used by breeders for marker assisted selection (MAS) of the nectariless trait. DNA markers associated with the genes conditioning the trait and used for MAS, will allow cotton cultivars to be easily developed that have decreased attractiveness to insects and reduce the need for insecticides, especially those harmful to beneficial insects such as honeybees.

Assessment of the Origin and Diversity of Croatian Common Bean Germplasm Using Phaseolin Type, SSR and SNP Markers and Morphological Traits

Landraces represent valuable genetic resources for breeding programmes to produce high-yielding varieties adapted to stressful environmental conditions. Although the common bean (Phaseolus vulgaris L.) is an economically important food legume for direct human consumption worldwide, common bean production in Croatia is based almost exclusively on landraces and there is no common bean breeding program. Information on phaseolin type and results of population structure and genetic diversity obtained by analysis of SSR and SNP markers, in combination with the morphological characterization of 174 accessions of 10 common bean landraces (morphotypes), enabled thorough classification of accessions. The accessions were classified into phaseolin type H1 (“S”) of Mesoamerican origin and phaseolin types H2 (“H” or “C”) and H3 (“T”) of Andean origin. By applying distance- and model-based clustering methods to SSR markers, the accessions were classified into two clusters at K = 2 separating the accessions according to the centres of origin, while at K = 3, the accessions of Andean origin were further classified into two clusters of accessions that differed in phaseolin type (H2 and H3). Using SNP markers, model-based analysis of population structure was performed, the results of which were consistent with those of SSR markers. In addition, 122 accessions were assigned to 14 newly formed true-type morphogenetic groups derived from three different domestication events: (1) Mesoamerican (H1A) (“Biser”, “Kukuruzar”, “Tetovac”, “Trešnjevac”), (2) Andean—indeterminate type (H2B1) (“Dan noć”, “Sivi”, “Puter”, ”Sivi prošarani”, “Trešnjevac”) and (3) Andean—determinate type (H3B2) (“Bijeli”, “Dan noć”, “Puter”, “Trešnjevac”, “Zelenčec”). The rest of the accessions could represent putative hybrids between morphogenetic groups. The differences between the true-type groups of accessions were further analysed based on nine quantitative traits, and the subsets of traits that best distinguish among centres of origin (A: Mesoamerican, B: Andean) and genetic groups (H1A, H2B1, H3B2) were proposed.

Association Mapping of Thousand Grain Weight using SSR and SNP Markers in Rice (Oryza sativa L.) Across Six Environments

Thousand grain weight (TGW) is an important determinant of rice yield, and correlates with grain size, plumpness and grain number per panicle. In rice, there are fewer association mapping studies relating grain weight traits using both SSR and SNP markers. In this study, in order to find robust SSR markers associated with TGW trait and mine elite accessions in rice, we investigated the TGW trait across six environments using a natural population consisted of 462 accessions, and then performed association mapping using both SSR and SNP markers. Using the six datasets from the six environments and their best linear unbiased estimator, we identified eight TGW associated SSR markers, with three environmentally stable and one newly found, on five chromosomes. The associated markers have genetic effect from 3.44% to 20.84%, and two of them carry stable elite allele with positive effect across different environments. Candidate interval association mapping using re-sequencing derived SNP/InDel markers further confirms the TGW-SSR association, and also suggests that 3 TGW-SSR associations were high confident in intervals of size from 176 to 603 kb. These results not only shed more lights on the genetics of TGW trait, but also suggest that the multi-allelic SSR markers should be used as an alternative power tool in gene or QTL mapping.

Assessment of heterosis based on parental genetic distance estimated with SSR and SNP markers in upland cotton (Gossypium hirsutum L.)

Background Heterosis has been extensively utilized in different crops and made a significant contribution to global food security. Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid breeding. The objectives of this study were to estimate the GD between parents using both simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) markers and to investigate the efficiency of the prediction of hybrid performance based on GD. The experiment comprised of four male parents, 282 female parents and 1128 F1, derived from NCII mating scheme. The hybrids, their parents and two check cultivars were evaluated for two years. Performance of F1, mid-parent heterosis (MPH), and best parent heterosis (BPH) were evaluated for ten agronomic and fiber quality traits, including plant height, boll weight, boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index. Results Heterosis was observed in all hybrids and, the traits like plant height, boll number, boll weight and lint percentage exhibited higher heterosis than the fiber quality traits. Correlations were significant between parental and F1 performances. The F1 performances between three hybrid sets (Elite×Elite, Exotic×Elite, and Historic×Elite) showed significant differences in eight traits, including boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index. The correlation of the GD assessed by both SSR and SNP markers was significantly positive. The cluster analysis based on GD results estimated using SNP showed that all the female parents divided into five groups and the F1 performance between these five groups showed significant differences in four traits, including lint percentage, micronaire, fiber strength, and fiber elongation ratio. The correlation between GD and F1 performance, MPH and BPH were significant for lint percentage and micronaire. Conclusions Our results suggested that GD between parents could be helpful in heterosis prediction for certain traits. This study reveals that molecular marker analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid cotton breeding.

Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

Assessment of heterosis based on parental genetic distance estimated with SSR and SNP markers in Upland cotton (Gossypium hirsutum L.)

Background: Heterosis has been extensively utilized in different crops and made a significant contribution to global food security. Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid breeding. The objectives of this study were to estimate the GD between parents using both simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) markers and to investigate the efficiency of the prediction of hybrid performance based on GD. The experiment comprised of four male parents, 282 female parents and 1128 F1, derived from NCII mating scheme. The hybrids, their parents and two check cultivars were evaluated for two years. Performance of F1, mid-parent heterosis (MPH), and best parent heterosis (BPH) were evaluated for ten agronomic and fiber quality traits, including plant height, boll weight, boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index. Results: Heterosis was observed in all hybrids and, the traits like plant height, boll number, boll weight and lint percentage exhibited higher heterosis than the fiber quality traits. Correlations were significant between parental and F1 performances. The F­1 performances between three hybrid sets (Elite×Elite, Exotic×Elite, and Historic×Elite) showed significant differences in eight traits, including boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index. The correlation of the GD assessed by both SSR and SNP markers was significantly positive. The cluster analysis based on GD results estimated using SNP showed that all the female parents divided into five groups and the F1 performance between these five groups showed significant differences in four traits, including lint percentage, micronaire, fiber strength, and fiber elongation ratio. The correlation between GD and F1 performance, MPH and BPH were significant for lint percentage and micronaire. Conclusions: Our results suggested that GD between parents could be helpful in heterosis prediction for certain traits. This study reveals that molecular marker analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid cotton breeding.

Assessment of Heterosis Based on Parental Genetic Distance Estimated With SSR and SNP Markers in Upland Cotton (Gossypium Hirsutum L.)

Background: Heterosis has been extensively utilized in different crops and made a significant contribution to global food security. Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid breeding. The objectives of this study were to estimate the GD between parents using both simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) markers and to investigate the efficiency of the prediction of hybrid performance based on GD. The experiment comprised of four male parents, 282 female parents and 1128 F1, derived from NCII mating scheme. The hybrids, their parents with two check cultivars were evaluated for two years. Performance of F1, mid-parent heterosis (MPH), and best parent heterosis (BPH) were evaluated for ten agronomic and fiber quality traits. Results: Heterosis was observed in all hybrids and, the traits like plant height, boll number, boll weight and lint percentage exhibited higher heterosis than the fiber quality traits. Correlations were significant between parental and F1 performances. The F­1 performances between three hybrid sets (Elite×Elite, Exotic×Elite, and Historic×Elite) showed significant differences in eight traits. The correlation of the GD assessed by both SSR and SNP markers was significantly positive. The cluster analysis based on GD results estimated using SNP showed that all the female parents divided into five groups and the F1 performance between these five groups showed significant differences in seven traits. The correlation between GD and F1 performance, MPH and BPH were significant for lint percentage and micronaire. Conclusions: Our results suggested that GD between parents could be helpful in heterosis prediction for certain traits. This study reveals that molecular marker analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid cotton breeding.